The Dewar valence isomer of the (6-4) photoadduct of thymidylyl-(3'-5')-thymidine monophosphate: formation, alkaline lability and conformational properties.

The formation of the Dewar valence isomer of the pyrimidine(6-4)pyrimidone photoadduct of thymidylyl-(3'-5')-thymidine monophosphate (TpT) was investigated under different irradiation conditions. This photoproduct was generated on exposure of TpT to far-UV radiation. However, no detectable amount of the Dewar isomer or its precursor (pyrimidine(6-4)pyrimidone photoadduct) was observed following acetone photosensitization of TpT. The Dewar valence isomer was much more unstable than the pyrimidine(6-4)pyrimidone photoproduct when treated with hot piperidine. A detailed conformational analysis of the TpT Dewar isomer photoproduct is reported as inferred from extensive one- and two-dimensional 300 and 620 MHz proton nuclear magnetic resonance (1H NMR) measurements and molecular mechanics calculations.     

The photochemistry of thymidylyl-(3'-5')-5-methyl-2'-deoxycytidine in aqueous solution

The photochemistry of the dinucleoside monophosphate thymidylyl-(3'-5')-5-methyl-2'-deoxycytidine (Tpm5dC) has been studied in aqueous solution using both 254 nm and UV-B radiation. A variety of dinucleotide photoproducts containing 5-methylcytosine (m5C) have been isolated and characterized. These include two cyclobutane dimers (CBD) (the cis-syn [c,s]and trans-syn forms), a (6-4) adduct and its related Dewar isomer, and two isomers of a product in which the m5C moiety was converted into an acrylamidine. Small amounts of thymidylyl-(3'-5')-thymidine (TpT) were also formed, presumably as a secondary photoreaction product. In addition, a photoproduct was characterized in which the m5C moiety was lost, thus generating 3'-thymidylic acid esterified with 2'-deoxyribose at the 5-hydroxyl on the sugar moiety. The c,s CBD of Tpm5dC readily undergoes deamination to form the corresponding CBD of TpT. The kinetics of this deamination process has been studied; the corresponding enthalpy and entropy of activation for the reaction have been evaluated at pH 7.4 as being, respectively, 73.4 kJ/mol and -103.5 J/K mol. Deamination was not observed for the other characterized photoproducts of Tpm5dC.     

DEGRADATION OF OLIGONUCLEOTIDES BY VACUUM-UV RADIATION IN SOLID: ROLES OF THE PHOSPHATE GROUP AND BASES

Abstract— Vacuum-UV induced degradation of deoxyoligonucleotides in solid form was studied by thin-layer chromatography with special emphasis on the fragmentation products. First, the degradation scheme previously proposed for 2'-deoxyadenylyl-(3'-5')-2'-deoxyadenosine (dApdA), which states that deoxypentose of the adenylyl moiety is the initial site of destruction, was confirmed by employing 258, 275, and 285 nm, in combination, as scanning wavelengths of chromatograms. Consistent results were obtained with 2'-deoxyadenylyl-(3'-5')-2'-deoxycytidine (dApdC), for which adenine and 5'-monophosphate of deoxycytidine are the predicted products, although the efficiency for such degradation mode was found to be lower with dApdC than with dApdA. Cytosine residue, thus, appeared to exert a suppressive effect on the destruction of deoxypentose of the adenylyl moiety. Second, with 2'-deoxycytidylyl-(3'-5')-2'-deoxyadenosine (dCpdA) the same spectroscopic analysis revealed that both adenine and cytosine were released, as well as some unidentified products, which could not be precisely identified by their chromatographic positions as dAMP or dCMP, although they showed characteristic absorption properties of adenine or cytosine containing species. This suggests that the photodegradation mode of dideoxynucleoside monophosphates is not so unique as hypothesized above, but that it depends also on the sequence of base residues. Finally, a very poor sensitivity to photodegradation of thymidylyl-(3'-5')-2'-deoxycytidine(dTpdC) and thymidylyl-(3'-5')-thymidine (dTpdT) to vacuum-UV radiation suggests that any pyrimidine could decrease the damaging effect of high energy vacuum-UV photons.     

Sugar conformational effects on the photochemistry of thymidylyl(3'-5')thymidine

The synthesis and conformational analysis of 2'-O,5-dimethyluridylyl(3'-5')-2'-O,5-dimethyluridine (1a), the analogue of thymidylyl(3'-5')thymidine (TpT; 1b) in which a methoxy group replaces each 2'-alpha-hydrogen atom, are described. In comparison with TpT, such modification increases the population of the C3'-endo conformer of the sugar ring puckering at the 5'- and 3'-ends from 30 to 75% and from 37 to 66%, respectively. Photolyses of 1a and TpT at 254 nm are qualitatively comparable (the cis-syn cyclobutane pyrimidine dimer and the (6-4) photoproduct are formed), although it is significantly faster in the case of 1a. These results are explained by the increased propensity of the modified dinucleotide to adopt a base-stacked conformation geometry reminiscent of that for TpT.     

Far-UV photochemistry and photosensitization of 2'-deoxycytidylyl-(3'-5')-thymidine: isolation and characterization of the main photoproducts.

Far-UV irradiation of 2'-deoxycytidylyl-(3'-5')-thymidine (dCpT) gave rise to the pyrimidine (6-4) pyrimidone adduct and its Dewar valence isomer as the main photoproducts. The absolute configuration of the former adduct was determined and its photoisomerization studied. A comparison of the alkali lability of both compounds showed that hydrolysis of the phosphodiester bond occurs for the Dewar valence isomer but not for its (6-4) precursor. In addition, the trans-syn and cis-syn cyclobutane dimers of dCpT were obtained by acetophenone photosensitization and characterized. Finally, the deamination rate constants for this series of compounds were shown to be dramatically influenced by the nature and the configuration of the photoproducts.     

ALKALI-LABILE PHOTOLESIONS MAPPING TO PURINE SITES IN ULTRAVIOLET-IRRADIATED DNA

Gel sequencing experiments with the 5'- and 3'-end-labeled oligonucleotides d(A₃GA₄GA₅GA₆GA₃G) and d(AT) ₁₀ have demonstrated that dimeric adenine photoproducts and thymine-adenine photoadducts constitute alkali-labile lesions in UV-irradiated DNA. On treatment with hot piperidine, DNA strand breakage occurs predominantly at the sites of 5'-adenines in the dimeric photoproducts and of 3'-adenines in the thymine-adenine photoadducts. With 5'-end-labeled oligonucleotides of mixed sequence, major UV-induced loci for alkaline cleavage map to purine bases flanked on their 5'-side by two pyrimidines. This behavior does not arise from enhanced photoreactivity of purines in this sequence context as has been inferred from photofootprinting studies. Instead, as shown by 3'-labeling and selective substitution with 5-methylcytosine, it results from the anomalous electrophoretic mobility of 5'-end-labeled fragments produced by alkaline cleavage of DNA at adjacent pyrimidine (6-4) pyrimidone photoproducts.     

Depopulation of Highly Excited Singlet States of DNA Model Compounds: Quantum Yields of 193 and 245 nm Photoproducts of Pyrimidine Monomers and Dinucleoside Monophosphates

Abstract— Formation of uracil and orotic acid photodimers, uridine and 5'-UMP photohydrates, TpT photodimers and (6-4)photoproducts, dCpT photohydrates and (6-4)photo-products and UpU, CpC and CpU photohydrates were studied in neutral deoxygenated aqueous solution at room temperature upon irradiation at either 193 or 254 nm. The photoproducts were identified and quantified and the contribution from photoionization to substrate decomposition, using λ_irr= 193 nm, was separated. The ratio of the quantum yields of respective stable products,η=φ¹⁹³/φ²⁵⁴ is indicative of the yield of internal conversion from the second to the first excited singlet state, S₂→ S₁. For the observed photodimers η decreases from 0.94 for uracil to 0.7 for TpT and further to 0.55 for orotic acid. For the (6-4)photoproducts of TpT and dCpT T| = 0.5-0.8 and for the photohydrates in the cases of UpU, CpC, CpU and dCpT TJ ranges from 0.55 to 1.     

The (α-4) photoconjugates of 5-methylcytosine, 1,5-dimethylcytosine, 1-methylthymine and thymidine

The pyrimidine nucleobases contained in DNA undergo a variety of photoinduced reactions in which two moieties become joined to form a product (e.g. formation of cyclobutane dimers and [6-4] adducts). Herein, we describe a new type of photoconjugation reaction that has been shown to occur for 5-methylcytosine (5-MeC), 1,5-dimethylcytosine (1,5-diMeC), 1-methylthymine and thymidine; in this reaction the 5-methyl group of one nucleobase (or nucleoside) becomes attached to the 4-position of the second moiety. For example, 5-MeC forms α-4'-(5'-methylpyrimidin-2'-one)-5-methylcytosine. The various (α-4) conjugates are produced upon irradiation of the parent compound in frozen aqueous solution at -78.5°C. The UV spectra of these compounds display a characteristic "double humped" profile, similar to that expected from overlaying the spectrum of parent nucleobase with that of a 2'-pyrimidone moiety. Preliminary results suggest that thymine and 5-methyl-2'-deoxycytidine (5-MedCyd) form analogous photoproducts. A variety of other previously unreported photoproducts are described as well for the 5-MeC, 1,5-diMeC and 5-MedCyd systems.     

THE PHOTOCHEMISTRY OF 14 C-5-BROMO-2''-DEOXYURIDYLYL-(3''→5'')-THYMIDINE DETERMINATION OF QUANTUM YIELDS AS A FUNCTION OF pH

Abstract— Quantum yields for the formation of the major photoproduct of 2-¹⁴C-5-bromo-2'-deoxyuridylyl-(3'→5')-thymidine (BrdUpT) have been determined by irradiation of the 2-¹⁴C-BrU-labeled dinucleotide at pH 2.3, 5.9, 7.05, 8.0 and 10.25 with U.V. light at 280nm. At acidic and neutral pH the quantum yield was 0.0063; the value decreased markedly above pH 8.0 to 0.0025 at pH 10.25. Some evidence of the formation of additional photoproducts at high and low pH was found. Some aspects of the mechanism of the reaction are discussed.
Consideration of p K_a values calculated for singlet and triplet excited states indicates that the decrease in the quantum yield of main photoproduct at high pH is due to dissociation of the excited bromodeoxyuridine moiety. It is suggested that the formation of BrdUpT photoproduct and the debromination of bromouracil-labeled DN A occur via different excited states.     

QUANTITATIVE CONVERSION OF THE (6–4) PHOTOPRODUCT OF TpdC TO ITS DEWAR VALENCE ISOMER UPON EXPOSURE TO SIMULATED SUNLIGHT

It has been found that the (6-4) photoproduct of thymidylyl-(3'----5')-deoxycytidine (TpdC) is converted quantitatively to a further photoproduct upon exposure to Pyrex-filtered medium pressure mercury arc light. Infrared UV, FAB MS, 1H NMR, 13C NMR and 31P NMR spectra were obtained for both the (6-4) product and its photolysis product. 1H NMR assignments were made on the basis of proton decoupling and homonuclear shift correlated experiments and 13C NMR assignments were made on the basis of proton-detected heteronuclear shift correlated experiments. The Dewar pyrimidinone structure was assigned to the photolysis product by analysis of the spectral data in comparison to those of the Dewar photoproduct of TpT and other Dewar pyrimidinones. The (6-4) product of TpdC is the second member of the class of (6-4) photoproducts that has been found to photoisomerize to its Dewar valence isomer upon exposure to wavelengths greater than 280 nm, the first being that of TpT (Taylor and Cohrs, 1987, J. Am. Chem. Soc. 109, 2834-2835). These results further support the proposal that all members of the (6-4) photoproduct class are converted to their Dewar valence isomers upon exposure to sunlight.     

3-CARBETHOXYPSORALEN-DNA PHOTOLESIONS: IDENTIFICATION AND QUANTITATIVE DETECTION IN YEAST AND MAMMALIAN CELLS OF THE TWO cis-syn DIASTEREOISOMERS FORMED WITH THYMIDINE

Abstract A chemical method for the identification and the quantitative detection of psoralen DNA furan-side photoadducts formed in cells is presented. It is based on an enzymatic digestion of the purified DNA extracted from the treated cells and a further separation by high performance liquid chromatography of the modified nucleosides coupled to a highly sensitive fluorescence analysis and detection. Using this method, 3-carbethoxypsoralen- DNA photoadducts formed in yeast and mammalian cells have been identified and quantified. The predominant photoadducts induced have been identified as two cis-syn dThd(⁵₆^4'_5')3-CPs diastereoisomers. In Chinese Hamster V79 cells treated with 3-carbethoxypsoralen at 50 μM and irradiated at 365 nm with an incident dose of 24 kJ/m², the two monoadducts could be quantitatively assessed at levels as low as 1.3 and 0.7 per 10 000 base pairs.     

The photochemistry of uracil: a reinvestigation

Results from a re-examination of the photochemical reactions undergone by uracil (Ura) are presented. Irradiation of Ura in frozen aqueous solution at -78.5°C produces two diastereomeric (6-4) products, namely the cis and trans isomers of 5-hydroxy-6-4'-(pyrimidin-2'-one)-5,6-dihydrouracil. Upon heating in 0.1m HCl, each of these compounds decomposes to form 6-4'-(pyrimidin-2'-one)uracil. In addition, evidence for production of a hydrate of a trimer of Ura is presented, Irradiation of this compound at 254nm forms Ura and a (6-4) adduct as products. The compounds 5-4'-(pyrimidin-2'-one)uracil and 6-hydroxy-5,6-dihydrouracil were also present after Ura was irradiated in frozen aqueous solution. Cyclobutane dimers (CBDs) are formed when Ura is irradiated in the frozen aqueous state, in fluid aqueous and acetonitrile solution and in the presence of photosensitizers (e.g. acetone). Published information, concerning the identity and relative quantitative importance of the four CBD isomers (cis-syn, cis-anti, trans-syn and trans-anti) formed in these photochemical systems, is incomplete and often in substantial disagreement. Using chemical methods in conjunction with HPLC, the identity and relative amounts of the four dimers have been determined in each of these systems. Consequently, a number of inconsistencies found in the literature concerning dimer product identity and quantitative distribution have been resolved.     

Crystal structure and photochemical behavior in solution of the 3'-N-sulfamate analogue of thymidylyl(3'-5')thymidine

The 3'-N-sulfamate analogue of thymidylyl(3'-5')thymidine (TnsoT, 1) exhibits a preference for a C3'-endo conformation in the solution and solid states. Its photochemical behavior in solution is compared to that of its natural counterpart, thymidylyl(3'-5')thymidine (TpT, 2), to get further insight into the significance of the C3'-endo conformation on the photoproduct formation at the single-stranded dinucleotide level. Irradiation at 254 nm of 1 led to the same type of photoproducts as observed with 2. However, 1 was significantly more photoreactive than 2, and accordingly, the initial rate of photoproduct formation was enhanced in accordance with its propensity to base stack compared to 2. The corresponding quantum yields were determined and showed that the enhancement factor (1 compared to 2) is moderate for the cyclobutane pyrimidine dimer (CPD) (1.26) and much higher for the (6-4) photoproduct (1.8). These data strongly suggest that the CPD and (6-4) photoproduct arise from distinct minor stacked conformations.     

Investigation of the Reaction of N-Acetylindoxyl with Substituted Anilines. Synthesis of Derivatives of Indolo[3,2-b]quinolines

1-Acetyl-2,3-dihydrospiro[indolo-3,2'-(1',2',3',4'-tetrahydroquinazolin-4'-one) was obtained from the reaction with anthranilamide, and 3-(2'-acetylaminophenyl)quinoxalin-2-one from the reaction with o-phenylenediamine, along with the normal products of the condensation of N-acetylindoxyl with substituted anilines. Derivatives of indolo[3,2-b]quinoline were synthesized from the obtained condensation products.     

PHOTOLESIONS IN DNA UPON 193 nm EXCITATION

Aqueous solutions of plasmid (pBR322 and pTZ18R) and calf thymus DNA were excited by 20 ns laser pulses at 193 nm. The quantum yields of single- and double-strand break formation, interstrand cross-links, locally denatured sites, (6–4)photoproducts and biological inactivation (Φ_ssb, Φ_dsb, Φ_icl, Φ_ids, Φ_6–4 and Φ_ina, respectively) were measured. The quantum yields are virtually independent of intensity, demonstrating a one-quantum process. The obtained values in aerated neutral solution in the absence of additives are Φ_ssb= 1.5 × 10^--³, Φ_dsb, = 0.06 × 10^--³ (dose: 10–200 J m^-2), Φ_icl=Φ_Ids= 0.1 × 10³ and Φ_6–4= 0.5 × 10^--³ Both Φ_ssb and Φ_dsb decrease strongly with increasing concentrations of TE buffer (0.01–10 m M ). Biological inactivation of the pTZ18R plasmid was determined from the transformation efficiency of Escherichia coli bacteria strains AB1157, AB1886 uvr and A82480 uvr rec; the Φ_ina values are 1.4 × 10³, 2.1 × 10³ and 3 × 10^--³, respectively. The monoexponential survival curves in all cases show that a single damage site leads to inactivation (one single hit). The biological consequences of different photoproducts are discussed.     

Identification of the alpha and beta anomers of 1-(2-deoxy-D-erythro-pentofuranosyl)-oxaluric acid at the site of riboflavin-mediated photooxidation of guanine in 2'-deoxyguanosine and thymidylyl-(3'-5')-2'-deoxyguanosine

Products of riboflavin-mediated photosensitization of 2'-deoxyguanosine (dG) and thymidylyl-(3'-5')-2'-deoxyguanosine (TpdG) by 350-nm light in oxygen-saturated aqueous solution have been isolated and identified as 1-(2-deoxy-beta-D-erythro-pentofuranosyl) oxaluric acid (beta-dOx) and thymidylyl-(3'-5')-1-(2-deoxy-beta-D-erythro-pentofuranosyl) oxaluric acid (Tpbeta-dOx), respectively. In aqueous solution the modified beta-deoxyribonucleoside is slowly converted to the alpha-anomer, generating alpha-dOx and Tpalpha-dOx. These modified nucleosides and dinucleoside monophosphates have been isolated by HPLC and characterized by proton and carbon NMR spectroscopy, fast atom bombardment mass spectrometry, and enzymatic analyses. Both alpha-dOx and Tpalpha-dOx slowly convert back into the modified beta-deoxyribonucleoside, indicating that the furanosidic anomers are in dynamic equilibrium. Relative to TpdG, the rate of hydrolysis of Tpbeta-dOx and Tpalpha-dOx by spleen phosphodiesterase is greatly reduced. Hot piperidine (1.0 M, 90 degrees C, 30 min) destroys Tpbeta-dOx and Tpalpha-dOx. Riboflavin-mediated photosensitization of TpdG in D2O instead of H2O has no detectable effect on the yield of Tpbeta-dOx, suggesting that oxaluric acid is generated through a Type-I reaction mechanism, likely through the intermediary on initially generated 8-oxo-7,8-dihydro-2'-deoxyguanosine.     

PROPERTIES OF AN UNUSUAL PHOTOPRODUCT OF U.V. IRRADIATED THYMIDYLYL-THYMIDINE

Abstract— One of the four major photoproducts formed by UV irradiation of TpT in aqueous solution has a number of unusual properties. This compound, which we arbitrarily call TpT⁴, is produced irreversibly from TpT with single-hit kinetics and seems to represent a novel pathway for TpT photolysis different from the conventional cyclobutane ring dimer formation. This communication describes the preparative isolation of TpT⁴ by ion-exchange chromatography on DEAE-cellulose and its UV, fluorescence and IR spectra. TpT⁴ has an absorption maximum at 325 mμ, fluoresces at 405 mμ when excited at 325 mμ, and has an IR spectrum consistent with the assumption that one of the thymine rings has been converted to a pyrimidin-2-one structure. In addition, TpT⁴ appears to have both pyrimidine rings linked together and does not contain a peroxide group as previously supposed. Spectrophotometric titration shows that TpT⁴ has a pKâ of 10.75 and is unstable to prolonged treatment at extreme pH. A model structure consistent with the present data is given. This model contains the glycosidic and phosphodiester bonds intact with a 5-methylpyrimidine-2-one ring and a thymine ring joined in ether linkage at the C₄ positions, with an OH at the C₄ position in the thymine ring.     

TiCl4 catalyzed tandem construction of C-C and C-O bonds: a simple and one-pot atom-economical stereoselective synthesis of spiro-oxindoles

An atom-economical stereoselective synthesis of [{1-acetyl-5-methyl-6,8-dioxabicyclo(3.2.1)octane}-7-spiro-3'-(indolin-2'-one)] derivatives, containing both the oxindole and 6,8-dioxabicyclo(3.2.1)octane moieties via TiCl(4) catalyzed coupling of 2-acetyl-6-methyl-2,3-dihydro-4H-pyran with isatin derivatives is described.     

A LASER FLASH PHOTOLYSIS STUDY OF PYRENE-1-ALDEHYDE. INTERSYSTEM CROSSING EFFICIENCY, PHOTOREACTIVITY AND TRIPLET STATE PROPERTIES IN VARIOUS SOLVENTS

Abstract— Triplet-and singlet-related photoprocesses of pyrene-1-aldehyde (PA) in various solvents have been investigated in detail using 337.1 and 355 nm laser flash photolysis in conjunction with time-correlated determination of fluorescence lifetimes (τ_F) and steady-state photochemical and absorption-emission spectral measurements. In benzene, the lowest triplet of PA (43 < E_T < 46 kcal/mol) has a lifetime of about 50 µs (τ_T) and displays the absorption maximum at 443 nm with a maximum extinction coefficient (ε_max) of 21000 M ^-1cm^-1; the corresponding ketyl radical has a sharp absorption maximum at 428 nm (ε_max≥ 25000 M ^-1cm^-1). The quantum yields (φ_T) of lowest triplet occupation are high in nonprotic solvents (0.6–0.8), decrease in protic solvents (alcohols) as the polarity of the latter is increased, and maintain a complementary relationship with the quantum yields (φ_F) of fluorescence. Quantum yields (φ_PC) of loss of PA due to photoreactions in some solvents have also been determined under conditions of steady irradiation at 366 nm; φ_PC is in the range 0.1–0.2 in electron-rich olefinic solvents such as cyclohexene and tetramethylethylene. These results concerning τ_F, τ_T, φ_F. φ_T and φ_PC as well as the effects of 1,2,4-trimethoxybenzene and 2,5-dimethyl-2,4-hexadiene as quenchers for fluorescence, triplet yield, and photochemistry are discussed in the light of possible state orders for PA in polar and nonpolar environments.     

Controlled Double-Bond Migration in Palladium-Catalyzed Intramolecular Arylation of Enamidines

Palladium-catalyzed intramolecular cyclization of N-(N'-tert-butylformimidoyl)-6-[2-(2-iodophenyl)ethyl]-1,2,3,4-tetrahydropyridine (1a) and N-(N'-tert-butylformimidoyl)-6-[3-(2-iodophenyl)propyl]-1,2,3,4-tetrahydropyridine (1b) respectively results in formation of spiro compounds 1'-(N-tert-butylformimidoyl)-3',4'-dihydrospiro[indan-1,2'(1'H)-pyridine] (4a), 1'-(N-tert-butylformimidoyl)-1',6'-dihydrospiro[indan-1,2'(3'H)-pyridine] (5a), and 1'-(N-tert-butylformimidoyl)-5',6'-dihydrospiro[indan-1,2'(1'H)-pyridine] (6a) and 1'-(N-tert-butylformimidoyl)-3,3',4,4'-tetrahydrospiro[naphthalene-1(2H),2'(1'H)-pyridine] (4b), 1'-(N-tert-butylformimidoyl)-1',3,4,6'-tetrahydrospiro[naphthalene-1(2H),2'(3'H)-pyridine] (5b), and 1'-(N-tert-butylformimidoyl)-3,4,5',6'-tetrahydrospiro[naphthalene-1(2H),2'(1'H)-pyridine] (6b). The double-bond migration process can be controlled, and any of the three double-bond isomers can be prepared by employing proper ligands. A combination of BINAP and the amidine function was required to obtain the isomers 5a and 5b with the double bond in the homoallylic position relative to the aryl group. An electrospray ionization mass spectrometric study was conducted to support suggested reaction intermediates.